T_SELEX program: Theoretical SELEX tool for Rational Design and Selection of RNA Aptamers Targeting Macromolecules

T_SELEX program: Theoretical SELEX tool for Rational Design and Selection of RNA Aptamers Targeting Macromolecules | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article T_SELEX program: Theoretical SELEX tool for Rational Design and Selection of RNA Aptamers Targeting Macromolecules Kabelo Phuti Mokgopa, Kevin Alan Lobb, Tendamdzimu Tshiwawa This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5038044/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Selection of aptamers is crucial iterative process which is significant for many applications from biosensors to biomedical applications. The process of selecting aptamers is called systematic evolution of ligands by exponential enrichment (SELEX). This process is costly, time consuming and labour-intensive. In this communication we present T_SELEX API together with its algorithms and application. This program is an autonomous robust python package specifically engineered for designing aptamers and screening of RNA aptamers against macromolecular targets. The tool is evaluated from generation of sequence library of RNA aptamers, multiscale folding or secondary structure predictions, multiscale tertiary structure predictions, virtual screening and detailed analysis. The application was tested by screening a generated aptamer library against HIV-1 protease. The source code of the T_SELEX tool is available on GitHub [ https://github.com/CMCDD/T_SELEX ] and can be used directly following instructions on the readme file. Computational Chemistry Computational Biology Chemical Biology Aptamer RNA SELEX Virtual screening API and python package Full Text Additional Declarations The authors declare no competing interests. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5038044","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":350001652,"identity":"5576ad88-11d9-40fc-91fd-c2b3c212c984","order_by":0,"name":"Kabelo Phuti Mokgopa","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA2UlEQVRIiWNgGAWjYFADZuYDQFJChngdPOxsCSAtPCRo4ecxANMEVZq3H374uHKHjZw9M8/nVzdqLHgY2A8f3YBPi8yZNGPDs0CCh5l3m3XOMaDDeNLSbuDTIsGQwybZ2HY4sQeoxTiHDahFgscMvxb+N+w/gVrqe5h5nhnn/CNGi0QOGyNQSwIPMw/z49w2orQ8M5ZsPJNm2HOYzYw5t0+Ch42gX/iTH35s3GEjz95/+PHnnG91cvzsh4/h1QIGjA1gik0CTBJUjqSF+QNRqkfBKBgFo2DEAQB5qz8cX6P/yAAAAABJRU5ErkJggg==","orcid":"","institution":"Rhodes University","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Kabelo","middleName":"Phuti","lastName":"Mokgopa","suffix":""},{"id":350003677,"identity":"69e799d0-c060-414a-ba1f-2c8b8963099d","order_by":1,"name":"Kevin Alan Lobb","email":"","orcid":"","institution":"Rhodes University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Kevin","middleName":"Alan","lastName":"Lobb","suffix":""},{"id":350003678,"identity":"336cc5aa-296f-45a2-872e-d6744406cef9","order_by":2,"name":"Tendamdzimu Tshiwawa","email":"","orcid":"","institution":"Rhodes University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Tendamdzimu","middleName":"","lastName":"Tshiwawa","suffix":""}],"badges":[],"createdAt":"2024-09-05 12:07:23","currentVersionCode":1,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false,"coiExplicitlySet":false},"doi":"10.21203/rs.3.rs-5038044/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5038044/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":64063403,"identity":"17ce3a26-b991-4414-b554-1cfad1e98294","added_by":"auto","created_at":"2024-09-06 02:59:10","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":913760,"visible":true,"origin":"","legend":"","description":"","filename":"TSELEXpaper2024.15final.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5038044/v1_covered_7e1bdd03-41fa-45b0-ba94-8ad3dffb37fa.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eT_SELEX program: Theoretical SELEX tool for Rational Design and Selection of RNA Aptamers Targeting Macromolecules\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[{"identity":"da171938-d7bb-49b3-a6ff-e34a39be6a79","identifier":"10.13039/501100001321","name":"National Research Foundation","awardNumber":"PMDS22062928944","order_by":0}],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"Rhodes University","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Aptamer, RNA, SELEX, Virtual screening, API, and python package","lastPublishedDoi":"10.21203/rs.3.rs-5038044/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5038044/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eSelection of aptamers is crucial iterative process which is significant for many applications from biosensors to biomedical applications. The process of selecting aptamers is called systematic evolution of ligands by exponential enrichment (SELEX). This process is costly, time consuming and labour-intensive. In this communication we present T_SELEX API together with its algorithms and application. This program is an autonomous robust python package specifically engineered for designing aptamers and screening of RNA aptamers against macromolecular targets. The tool is evaluated from generation of sequence library of RNA aptamers, multiscale folding or secondary structure predictions, multiscale tertiary structure predictions, virtual screening and detailed analysis. The application was tested by screening a generated aptamer library against HIV-1 protease. The source code of the T_SELEX tool is available on GitHub [\u003ca href=\"https://github.com/CMCDD/T_SELEX\"\u003ehttps://github.com/CMCDD/T_SELEX\u003c/a\u003e] and can be used directly following instructions on the readme file.\u003c/p\u003e","manuscriptTitle":"T_SELEX program: Theoretical SELEX tool for Rational Design and Selection of RNA Aptamers Targeting Macromolecules","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-09-06 02:51:03","doi":"10.21203/rs.3.rs-5038044/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"f83568a4-3979-468d-a10e-5d8960bff1db","owner":[],"postedDate":"September 6th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":37151206,"name":"Computational Chemistry"},{"id":37151207,"name":"Computational Biology"},{"id":37151208,"name":"Chemical Biology"}],"tags":[],"updatedAt":"2024-09-06T02:51:03+00:00","versionOfRecord":[],"versionCreatedAt":"2024-09-06 02:51:03","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-5038044","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5038044","identity":"rs-5038044","version":["v1"]},"buildId":"cBFmMYwuxLRRLfASyISRj","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}